PDBsum entry 2j59

Hydrolase

PDB id: 2j59

Contents

Protein chains

(+ 0 more) 165 a.a. *

(+ 0 more) 113 a.a. *

Ligands

GTP ×6

DIO ×3

EDO ×3

SO4 ×6

Metals

_MG ×6

Waters ×1656

* Residue conservation analysis

PDB id:

2j59

Name:

Hydrolase

Title:

Crystal structure of the arf1:arhgap21-arfbd complex

Structure:

Adp-ribosylation factor 1. Chain: a, b, c, d, e, f. Fragment: delta 17-arf1, residues 17-180. Synonym: arf1. Engineered: yes. Mutation: yes. Rho-gtpase activating protein 10. Chain: m, n, o, p, q, r. Fragment: arf-binding domain, residues 929-1096.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606. Expression_system_taxid: 562

Resolution:

2.10Å R-factor: 0.209 R-free: 0.243

Authors:

J.Menetrey,M.Perderiset,J.Cicolari,T.Dubois,N.El Khatib,F.El Khadali, M.Franco,P.Chavrier,A.Houdusse

Key ref:

J.Ménétrey et al. (2007). Structural basis for ARF1-mediated recruitment of ARHGAP21 to Golgi membranes. EMBO J, 26, 1953-1962. PubMed id: 17347647 DOI: 10.1038/sj.emboj.7601634

Date:

13-Sep-06 Release date: 20-Feb-07

Protein chains

P84078  (ARF1_MOUSE) -  ADP-ribosylation factor 1 from Mus musculus

Seq: 181 a.a.

Struc: 165 a.a.*

Protein chains

Q5T5U3  (RHG21_HUMAN) -  Rho GTPase-activating protein 21 from Homo sapiens

Seq: 1958 a.a.

Struc: 113 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F: E.C.3.6.5.2 - small monomeric GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

GTP (Bound ligand (Het Group name = GTP) corresponds exactly) + H2O = GDP + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/sj.emboj.7601634

EMBO J 26:1953-1962 (2007)

PubMed id: 17347647

Structural basis for ARF1-mediated recruitment of ARHGAP21 to Golgi membranes.

J.Ménétrey, M.Perderiset, J.Cicolari, T.Dubois, N.Elkhatib, F.El Khadali, M.Franco, P.Chavrier, A.Houdusse.

ABSTRACT

ARHGAP21 is a Rho family GTPase-activating protein (RhoGAP) that controls the Arp2/3 complex and F-actin dynamics at the Golgi complex by regulating the activity of the small GTPase Cdc42. ARHGAP21 is recruited to the Golgi by binding to another small GTPase, ARF1. Here, we present the crystal structure of the activated GTP-bound form of ARF1 in a complex with the Arf-binding domain (ArfBD) of ARHGAP21 at 2.1 A resolution. We show that ArfBD comprises a PH domain adjoining a C-terminal alpha helix, and that ARF1 interacts with both of these structural motifs through its switch regions and triggers structural rearrangement of the PH domain. We used site-directed mutagenesis to confirm that both the PH domain and the helical motif are essential for the binding of ArfBD to ARF1 and for its recruitment to the Golgi. Our data demonstrate that two well-known small GTPase-binding motifs, the PH domain and the alpha helical motif, can combine to create a novel mode of binding to Arfs.

Selected figure(s)

Figure 1.
Figure 1 Structure of the ARF1:ArfBD complex. (A) A cartoon diagram of the ARF1:ArfBD complex is shown in two distinct orientations. ARF1 is shown in grey with the 1 helix and switch I region in light and dark blue, respectively, the interswitch region in green and the switch II region in red. The Mg.GTP ligand is shown as a grey stick model. ArfBD is shown in white with its 5' region ( 5' strand plus 5'– 6' loop) in pink, the 1' helix in orange and the Cter helix in yellow. Tyr999 and Ile1053 of ArfBD are shown as stick models. The two adjacent contact areas of the ARF1:ArfBD complex interface are delineated by black boxes on the right-hand view. (B) Detailed view of the interface between the Cter helix and the PH domain of ArfBD. (C–F) Detailed views of the ARF1:ArfBD interface. The secondary structures are shown as ribbons and the residues as sticks. Hydrogen bonds are indicated by dashed lines. (C) The 5' region of ArfBD (pink) lies between the interswitch (green) and switch I (blue) regions of ARF1 centred on Tyr999. (D) The network of water-mediated interactions made between Asp996 of the 5' region (in pink) of ArfBD and ARF1. (E) The switch I (blue) region of ARF1 interacts with the 5' region (pink) and the 1' helix (orange) of ArfBD. (F) The Cter helix (yellow) of ArfBD is grasped between the switch II (red) and the interswitch/switch I (green/blue) regions of ARF1.

Figure 2.
Figure 2 The hydrophobic pocket and triad patch of Arf proteins. (A) Front-view of the ARF1 hydrophobic pocket (transparent grey area) and the hydrophobic triad patch (transparent purple area) with the hydrophobic residue side chains shown as stick models. (B) Sequence alignment of the Arf proteins (nomenclature from Kahn et al, 2006) with residues of the hydrophobic pocket indicated with grey shading and those of the triad patch indicated in purple. Residues conserved with ARF1 are shown in bold.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 1953-1962) copyright 2007.

Figures were selected by the author.